Yniv Palti

Abstract The genome of the Swanson doubled haploid (DH) YY male line of rainbow trout was de novo assembled using the Canu pipeline, high-coverage PacBio long-read sequence data, Bionano optical maps, and Hi-C proximity ligation sequence data, resulting in 29 major scaffolds aligning with the karyotype of the Swanson line (2 N = 58). This assembly, totaling 2.3 Gb with an N50 of 52.4 Mb, represents approximately 95% of the genome in 29 chromosome sequences with only 109 gaps between scaffolds.

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Abstract Cutthroat trout (Oncorhynchus clarkii) are popular among anglers throughout their native range along the West Coast and interior of North America. As they colonized the interior of North America, cutthroat trout diverged into several genetically distinct groups. Many of these groups are now threatened by habitat destruction, hybridization with rainbow trout (O. mykiss), and competition from introduced species.